package com.utilities.parsers;

import java.util.ArrayList;
import com.utilities.dataStructures.Range;

public class test {

	/**
	 * @param args
	 * @throws Exception 
	 */
	public static void main(String[] args) throws Exception 
	{
		String workspace = "C:/Users/bansalp/home/Desktop/UZH/newCosmid/run1run2/all/";
		String inputcontigsfile = workspace + "contigs.fna";
		String outputSegmentFile = workspace + "NewSegments.txt";
		PrimeFinder finder = new PrimeFinder();
		ArrayList<Range> genes = finder.find(inputcontigsfile,outputSegmentFile);

		MapperContigStats contigStats = new MapperContigStats(true, workspace + "contigs.fna", workspace + "scaffold.txt", 
				workspace + "gapList.txt", workspace + "contigList.txt", workspace + "vxml_new.xml");
		contigStats.setGeneList(genes).main(null);
	}
}
